Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107964
Name   oriT_2019-04-28369-1-2|4 in_silico
Organism   Providencia alcalifaciens strain 2019-04-28369-1-2 isolate 2019-04-28369-1-2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OU659123 (572..606 [+], 35 nt)
oriT length   35 nt
IRs (inverted repeats)      9..15, 19..25  (GCAAAAT..ATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 35 nt

>oriT_2019-04-28369-1-2|4
AAATTCTTGCAAAATGAAATTTTGCGTAGTGTGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5342 GenBank   WP_224051218
Name   traI_LDO76_RS20620_2019-04-28369-1-2|4 insolico UniProt ID   _
Length   1708 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1708 a.a.        Molecular weight: 187773.80 Da        Isoelectric Point: 5.7090

>WP_224051218.1 conjugative transfer relaxase/helicase TraI [Providencia alcalifaciens]
MLTVAPIANNAANYYTHEDNYYFLGNLEARWMGEGAKSLGLEGEVTKDQLGEILEGRLPNDQSLERMENG
KNVHREGHDLTFSAPKSVSVLGIVLGDKRMIEAHNRAVEVALHEVEGLASTRMMVEGKTSLEMTKNLVVA
AFNHDTSREHDPQLHTHALVMNMTEHNGEWRTLSSDTRSKMGFSEALYDLRIALGEIYQNTLRKEIEGMG
FKTHNAGRNSLWEIDGVPVTPFSQRRQQILDAVGHEASLKSRDVAALDTRQAKTTPEKSELLTDWFDRLE
KNSFGADARKSFYAEAEQRLAKGQMGDASRDIQPDITRAVTDAIALLSDKQLSMTYSQVLAKTLGGLEAR
AGMIAQVREAIDVAIEQRQLIPLDEKKGLFTSSIHLMDELKLQQIATDMKQHNRTVSFQARTEALSPVME
KVADTLPSIAIVASQGLGKAQRDGVLDGITMAQSQGRDVAVMTLDTTSRQAFANDKRFAYVPKMTLGDGQ
PLKPNSTLVVANAEKLSLKSALSLLESAQSANVQVLMMDSGGRKGTGNVLATLQDAGVPRFQGESSAVLT
VKTAHIPDKNHRYAALAAEYAQLHSDMKSVVAQVSGVREQKIVTDTIRQTLTERGMLSEKTVTVTQLKPV
WLDSHSRKQIDSYREGMVMERWNADKKEVERYTIDRVTPETRSVTLLDSQGQKQVMKPQQFDGQWSAYQR
QTMDIAQGEQLTILAKQNKLSARDAVTVTGFMPNAIMVNFNGKTHRIDVRDGVKADYGYVTVPGQQANDT
GTVLLAASARDTQPTLLNTVARSGEHITVYTPLDKMETERRLSRSPVYQQARQLAGVEGLDSKAIEQAAD
KATEALLSKPEKALQQGMALAQESQVFFSRIDAIAKALPLHNSLDSQSLGKAFDRLVAQKAIIPVTSGKG
AAQQHYVTASTWAMEKQILTTILAGKDTQAPLMASVPEAQLNGLTSGQKAATELILGSRDQFVGIQGYAG
VGKTTQFTAVLKALDTLPATQRPEVIGLAPTHRAVGEMAAVGVKAQTLQAFLMDANQRQQLGETLDFKNT
LFLVDESSMIGNRNLSEVLQIIAQGGGRGVLSGDTAQLLSVDSGTPFALAQDRSALDTAIMKEIVRQNPE
LRPAIEAIIAGQVQMAMDTMNSVTPDVVPRRAGAELPEQSVIDAGDRVIARILDDYRGRTPEAQKETLIV
VQTNVDKDVINSGIHDILIEQGQLQGGKFVPILVRENTRTEALLSTAGMAEHAGKIALIQEQYYRIEVTQ
EGVSDGVVTLVDEQGKGHLLSAFESSLRDIGIYRQEARHIAAGEKINFTRTDKERGRVMNSDWTVSEVNE
HGQITLTNGEESRVLDPNSELTDQHLDYGYAGTAYKAQGASSPYVIVLGGVELGRRMLATLRDAYVALSR
TKAHVQTYSDDLDKWTSKITNPGNRKTAHDVLLAEQDYAAKVGNQLFDHAKPLNDTAIGRALSRQMGLGE
SHEGKFVYPSTKHPEPHVAWPAYDVHGKAQGTVLQAIELEGDKLQGLRTEGRLLGSEQAQFIVVKPSQNG
HTVIVNSLESAFETMAQQPEQGVVVQLNPDERLHTTMIEKITQGEVDNAYANPNTAQTDKADSDPKNLQT
PEEQAIDNALKEAEAALRQQANGEPKVPELSEDELRQVMAQERDSLLKGEHDLMEAKERVIEKAVQFERE
HQQQQRDVLRQQEREMVMEKTRDREFGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(627-705)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(568-619)

TrwC relaxase (TrwC)

(8-280)

AAA domain (AAA_30)

(954-1141)

DNA helicase TraI (TraI_C)

(1396-1508)


  Protein structure



No available structure.




T4CP

ID   5621 GenBank   WP_282563892
Name   traD_LDO76_RS20625_2019-04-28369-1-2|4 insolico UniProt ID   _
Length   742 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 742 a.a.        Molecular weight: 84918.85 Da        Isoelectric Point: 5.1648

>WP_282563892.1 type IV conjugative transfer system coupling protein TraD [Providencia alcalifaciens]
MSSTKHITQGGQVFSYMLGMFMQVNKRISFWLILLFLMIFPIIFYFKVPLQEIKNGGLYWWLYLTAGGEK
ALYRVAPIYEVDFDGQLYRFTSDAILKDDYMIYAGNIVLQELGLSLLWACIIVIVLFFVIYRVFHGLGKR
QANDDVIGGRTLTEDIKHVRNMLHARREASPITFDGLPLKLNSEVQNMLMHGTPGSGKSNTINKLLIQLR
KRGDMVIVFDKGCSLVKRHYNENIDKLLNPLDERCENWDLWGECLTTPDFDSVANTLIPQSTSEDPFWTG
SARTIFTTVAAKLGSDDQRSYNKLLRTLLAIDLKSLRAYVEKTEASNLMEEKVEKTAISIRGVLTNYVKA
LRYLQGIERNGKAPFAIREWMKSVNEPKQRQGWLWITSNARQHESLKPLISMWLAQAANCLLEMGENPER
RVWFIYDELASLHKLPELPQVLSEARKFGGCFILGFQNKPQLDYTYGHDYANAMMDLLNTRFFFRSPDES
VAKWVRDQLGQTRKKVASEQYSFGPETVRDGVSFSKQQEDVDLVNYSDVQSLPDLDCYITLPGQYPVVKI
SMRYEKIKPIAAEFTPRPINDSLDQEIEAEIKSRMQDDALPAVMNQIIDNLISGKPIETPVDTAQNNTAL
EVTQTQPQSTVELTSQSVTQNSTPITTETAASDNPPENQGGQEVIIDNVKVNTETGEILGRVIDEEQNPQ
DLYDSYTRMRQDEKEIFNRPKPSQEKPKHINDDHDEPEMWWC

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-562)

  Protein structure



No available structure.



ID   5622 GenBank   WP_224051197
Name   traC_LDO76_RS20715_2019-04-28369-1-2|4 insolico UniProt ID   _
Length   903 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 903 a.a.        Molecular weight: 101474.94 Da        Isoelectric Point: 6.5159

>WP_224051197.1 type IV secretion system protein TraC [Providencia alcalifaciens]
MNEKPSLIDKLLAPFLPKSKDIVFDDEPEPVSLQEALFKNLFTAWREPDGNKRAAEALENMDYPSFCSLL
PYRNYDAKSGLFINKTTIGFALECTPLVGANEKIVDALDYFLRNKLPRKIPLTFMLLGSKCISEQLGYGL
KDFGWQGEEAEKFNHITRAFYERGALVGLDNKLNLPLSLRNYRLFVCYAEEHKKADALTLQKVNQILSIV
MKSLAGASLHCEQMNDKGLLQLVREISNFRHDQIALPSSQVDPYESLNDQCADRSLTLEIRPDAIHQSLS
MGKGQKSQTRIMNYMLEKNPTQFALWQTGDNLSNLLDPASSVSCPFAITMTVYVEDLVKTQNEAKKKFIT
NNSRANSKYINWVPGVKRKAEEWGALREGLDTNQMALARYSYGITLFCEDDDDKALEAEMALMNTYTTNH
LKLCPPTFMQLRNYLALFPFVMQEGLWGDMVRSGGTLRAKAFNVANLLPVVADNRICQKGLPIPSYRHQL
SFLDIFERGSGLGNDNFNAAVCGTSGSGKSFLMQALIRQVLDAGGWAYVLDMGDSYKELCHSLGGVYVDA
RDLKFNPFAGVVDIKETAESIRDLLIVLANPSGDMDDVSKSILLNAVQEVWEGKGPNGRKGNKVLIDDVH
DYLEAEVKAAYFDPQSTVQNKMQEIIVALKKYTTKGLYGEYFNSDKPALNEQVRFTVLEMGGLQNKPDLL
AAVMFSMMIFIQQRMYLTARSIKKLAAIDEGWKLLDNKSRFVADFIESGYRTARKYGGSYITISQGIDDF
DGDGASTAAKAAWSNSSFKIILRQNMEAFRKYNQKNPDQFNPVERAIIEGFPAAGDAHFSAFMLRIAGRS
SFHRLVTDPISRALYSTDGDDFQFRENLMAEGLSQQAALLALAKRKFPQEMETLSQWQSQTRH

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(319-471)

TraG P-loop domain (P-loop_TraG)

(505-795)

TraC protein (TraC_F_IV)

(64-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28100..55286

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO76_RS20625 (NVI2019_PLFLNFOB_04146) 28106..30328 - 2223 WP_224051219 type IV conjugative transfer system coupling protein TraD -
LDO76_RS20630 (NVI2019_PLFLNFOB_04147) 30540..30929 - 390 WP_155251352 hypothetical protein -
LDO76_RS20635 (NVI2019_PLFLNFOB_04148) 30984..31190 - 207 WP_036965596 TraR/DksA C4-type zinc finger protein -
LDO76_RS20640 (NVI2019_PLFLNFOB_04149) 31311..32039 - 729 WP_036965594 complement resistance protein TraT -
LDO76_RS20645 (NVI2019_PLFLNFOB_04150) 32218..35106 - 2889 WP_051473561 conjugal transfer mating-pair stabilization protein TraG traG
LDO76_RS20650 (NVI2019_PLFLNFOB_04151) 35119..36495 - 1377 WP_036965592 conjugal transfer pilus assembly protein TraH traH
LDO76_RS20655 (NVI2019_PLFLNFOB_04152) 36692..37087 - 396 WP_224051220 hypothetical protein -
LDO76_RS21715 (NVI2019_PLFLNFOB_04153) 37084..37512 - 429 WP_036965590 hypothetical protein -
LDO76_RS20665 (NVI2019_PLFLNFOB_04154) 37524..38048 - 525 WP_071992030 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO76_RS20670 (NVI2019_PLFLNFOB_04155) 38054..38353 - 300 WP_036965586 hypothetical protein -
LDO76_RS20675 (NVI2019_PLFLNFOB_04156) 38512..39447 + 936 WP_036965584 hypothetical protein -
LDO76_RS20680 (NVI2019_PLFLNFOB_04157) 39435..39827 - 393 WP_036965583 hypothetical protein -
LDO76_RS20685 (NVI2019_PLFLNFOB_04158) 39842..40630 - 789 WP_224051192 type-F conjugative transfer system pilin assembly protein TraF -
LDO76_RS20690 (NVI2019_PLFLNFOB_04159) 40627..42471 - 1845 WP_224051193 conjugal transfer protein TraN -
LDO76_RS20695 (NVI2019_PLFLNFOB_04160) 42471..43088 - 618 WP_224051194 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO76_RS20700 (NVI2019_PLFLNFOB_04161) 43104..44099 - 996 WP_036965577 conjugal transfer pilus assembly protein TraU traU
LDO76_RS20705 (NVI2019_PLFLNFOB_04162) 44096..44728 - 633 WP_224051195 type-F conjugative transfer system protein TraW -
LDO76_RS20710 (NVI2019_PLFLNFOB_04163) 44738..45163 - 426 WP_224051196 type-F conjugative transfer system protein TrbI -
LDO76_RS20715 (NVI2019_PLFLNFOB_04164) 45139..47850 - 2712 WP_224051197 type IV secretion system protein TraC virb4
LDO76_RS20720 (NVI2019_PLFLNFOB_04165) 47852..48415 - 564 WP_224051198 type IV conjugative transfer system lipoprotein TraV traV
LDO76_RS20725 (NVI2019_PLFLNFOB_04166) 48462..49340 + 879 WP_070929355 hypothetical protein -
LDO76_RS21720 (NVI2019_PLFLNFOB_04167) 49311..49628 - 318 WP_224051199 hypothetical protein -
LDO76_RS20735 (NVI2019_PLFLNFOB_04168) 49713..50114 - 402 WP_036965569 hypothetical protein -
LDO76_RS20740 (NVI2019_PLFLNFOB_04169) 50207..50503 - 297 WP_036965567 hypothetical protein -
LDO76_RS20745 (NVI2019_PLFLNFOB_04170) 50530..50805 - 276 WP_036965565 hypothetical protein -
LDO76_RS20750 (NVI2019_PLFLNFOB_04171) 50814..51170 - 357 WP_036965564 hypothetical protein -
LDO76_RS20755 (NVI2019_PLFLNFOB_04172) 51172..51510 - 339 WP_036965562 hypothetical protein -
LDO76_RS20760 (NVI2019_PLFLNFOB_04173) 51531..52022 - 492 WP_036965560 transcription/translation regulatory transformer protein RfaH -
LDO76_RS21725 (NVI2019_PLFLNFOB_04174) 52029..52223 - 195 WP_036965558 hypothetical protein -
LDO76_RS20770 (NVI2019_PLFLNFOB_04175) 52293..53654 - 1362 WP_224051200 TrbI/VirB10 family protein traB
LDO76_RS20775 (NVI2019_PLFLNFOB_04176) 53641..54414 - 774 WP_036965555 type-F conjugative transfer system secretin TraK traK
LDO76_RS20780 (NVI2019_PLFLNFOB_04177) 54398..54967 - 570 WP_036965554 type IV conjugative transfer system protein TraE traE
LDO76_RS20785 (NVI2019_PLFLNFOB_04178) 54981..55289 - 309 WP_224051201 type IV conjugative transfer system protein TraL -
LDO76_RS20790 (NVI2019_PLFLNFOB_04179) 55305..55673 - 369 WP_036965551 type IV conjugative transfer system pilin TraA -
LDO76_RS20795 (NVI2019_PLFLNFOB_04180) 55947..56138 - 192 WP_036965549 TraY domain-containing protein -
LDO76_RS20800 (NVI2019_PLFLNFOB_04181) 56179..56898 - 720 WP_036965547 hypothetical protein -
LDO76_RS20805 (NVI2019_PLFLNFOB_04182) 57036..57353 - 318 WP_036965545 hypothetical protein -

Host bacterium

ID   8399 GenBank   NZ_OU659123
Plasmid name   2019-04-28369-1-2|4 Incompatibility group   -
Plasmid size   57474 bp Coordinate of oriT [Strand]   572..606 [+]
Host baterium   Providencia alcalifaciens strain 2019-04-28369-1-2 isolate 2019-04-28369-1-2

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -